In this work, poly(methacrylic acid) (PMAA)-based molecularly imprinted polymer nanoparticles (MIP NPs) using isosorbide dinitrate (ISDN) as a template were prepared via a precipitation polymerization. The morphology and performance of the samples were investigated by varying different concentrations of azobisisobutyronitrile (AIBN) as an initiator. The MIP NP sample characterization as a function of the initiator concentration was evaluated utilizing Fourier transform infrared (FTIR) spectroscopy and field emission-scanning electron microscopy (FE-SEM) analyses. Regarding the washed MIP NP samples, the FTIR spectra results showed two main characteristic peaks located at 3339 and 1734 cm−1 wavenumbers corresponding to hydroxyl (–OH) and carbonyl (–C=O) groups, respectively. The intensity of these main peaks for the washed MIP NPs was higher than that of those for unwashed MIP NPs in which the active sites were appropriately formed between the polymer and template. These observations were occurred at the maximum amount of AIBN concentration (3 mmol). Moreover, the FE-SEM micrograph images exhibited an average diameter of approximately 40 nm for the MIP NP sample prepared with a low concentration of the initiator (0.5% of polymerizable double bonds). Furthermore, another two key factors for the MIP NPs such as binding capacity, and surface area using Barrett–Joyner–Halenda (BJH) method were studied to apply them for drug delivery systems potentially. On the other hand, the release of ISDN from MIP NP was considered through phosphate buffer saline (PBS, pH 7.4) at 37 °C for 5 days. The results showed higher ability of the sample compared with the non-imprinted polymer (NIP) ones to control the drug release, and kinetic trend of the drug absorption within the MIP NPs followed the pseudo-first model. Finally, the obtained outcomes showed that the low amounts of the initiator concentration have an indispensable role on the physicochemical properties of the synthesized MIP NPs.